Variant 14-89162657-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_005197.4(FOXN3):c.1164G>T(p.Gly388Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 1,613,962 control chromosomes in the GnomAD database, including 130 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0082 ( 12 hom., cov: 31)

Exomes 𝑓: 0.010 ( 118 hom. )

Consequence

FOXN3
NM_005197.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.713

Variant links:

Genes affected

FOXN3 (HGNC:1928): (forkhead box N3) This gene is a member of the forkhead/winged helix transcription factor family. Checkpoints are eukaryotic DNA damage-inducible cell cycle arrests at G1 and G2. Checkpoint suppressor 1 suppresses multiple yeast checkpoint mutations including mec1, rad9, rad53 and dun1 by activating a MEC1-independent checkpoint pathway. Alternative splicing is observed at the locus, resulting in distinct isoforms. [provided by RefSeq, Jul 2008]

FOXN3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 14-89162657-C-A is Benign according to our data. Variant chr14-89162657-C-A is described in ClinVar as [Benign]. Clinvar id is 2644444.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.713 with no splicing effect.

BS2

High AC in GnomAd4 at 1247 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXN3	NM_005197.4 linkuse as main transcript	c.1164G>T	p.Gly388Gly	synonymous_variant	6/6	ENST00000557258.6	NP_005188.2	O00409-2
FOXN3	NM_001085471.2 linkuse as main transcript	c.1230G>T	p.Gly410Gly	synonymous_variant	7/7		NP_001078940.1	O00409-1A0A024R6I1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXN3	ENST00000557258.6 linkuse as main transcript	c.1164G>T	p.Gly388Gly	synonymous_variant	6/6	1	NM_005197.4	ENSP00000452005.1		O00409-2

Frequencies

GnomAD3 genomes

AF:

0.00821

AC:

1247

AN:

151960

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00164

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00190

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000209

Gnomad FIN

AF:

0.0221

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0132

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00758

AC:

1895

AN:

250000

Hom.:

AF XY:

0.00741

AC XY:

1002

AN XY:

135234

show subpopulations

Gnomad AFR exome

AF:

0.00209

Gnomad AMR exome

AF:

0.00237

Gnomad ASJ exome

AF:

0.00318

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.0195

Gnomad NFE exome

AF:

0.0113

Gnomad OTH exome

AF:

0.00847

GnomAD4 exome

AF:

0.0103

AC:

15025

AN:

1461884

Hom.:

118

Cov.:

AF XY:

0.0100

AC XY:

7297

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00164

Gnomad4 AMR exome

AF:

0.00244

Gnomad4 ASJ exome

AF:

0.00302

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000197

Gnomad4 FIN exome

AF:

0.0215

Gnomad4 NFE exome

AF:

0.0118

Gnomad4 OTH exome

AF:

0.00798

GnomAD4 genome

AF:

0.00820

AC:

1247

AN:

152078

Hom.:

Cov.:

AF XY:

0.00822

AC XY:

611

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.00164

Gnomad4 AMR

AF:

0.00190

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000209

Gnomad4 FIN

AF:

0.0221

Gnomad4 NFE

AF:

0.0132

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00857

Hom.:

Bravo

AF:

0.00599

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.0116

EpiControl

AF:

0.00942

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

FOXN3: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

7.4

DANN

Benign

0.59

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over